tbuckley/cabot-search huggingface dataset:
Abstract IA015: Combined single cell atlasing and organoid modeling reveal progressive plasticity during human colorectal cancer metastasis
Authors: Karuna Ganesh
Journal: Cancer Research (2022)

Abstract Metastatic cancers invariably relapse due to the emergence of therapy resistant subclones that are capable of self-renewal, slow cell-cycling, tumor re-initiation and therapy resistance. However, the molecular mechanisms that underpin the phenotypic plasticity of metastasis stem cells, their relationship to tumor initiating cancer stem cells and macrometastasis, and the co-evolution of the immune response to dynamically emerging tumor regenerative states are not understood. We are adopting a patient-derived functional biospecimen approach combining (1) hypothesis-generation using transcriptomics, epigenomics and spatial/histological analysis of patient samples of primary and metastatic gastrointestinal (GI) cancer with (2) mechanistic dissection in cutting-edge patient-derived organoid models, including co-cultures with immune/stromal cells, and (3) genetically engineered and orthotopic transplantation models of metastatic GI cancer. By profiling, lineage tracing and genetically interrogating the evolving transcriptomic and chromatin landscapes of regenerative metastatic states, we are defining the molecular mechanisms that underpin the phenotypic plasticity of metastatic cancer, and the co-evolution of the tumor microenvironmental response to dynamically emerging tumor regenerative states. Our approach is unveiling crucial signaling nodes required for metastatic plasticity that can be therapeutically targeted to improve outcomes for patients with advanced cancer. Citation Format: Karuna Ganesh. Combined single cell atlasing and organoid modeling reveal progressive plasticity during human colorectal cancer metastasis [abstract]. In: Proceedings of the AACR Special Conference on Colorectal Cancer; 2022 Oct 1-4; Portland, OR. Philadelphia (PA): AACR; Cancer Res 2022;82(23 Suppl_1):Abstract nr IA015.
Abstract B016: Inhibition of KRASG12C in colon cancer illustrates a link between beta-catenin, WNK, and the GID complex
Authors: Kasturi Nayak, Yeonjoo Hwang, LeeAnn Wang, Danielle L. Swaney, Nevan J. Krogan, John D. Gordan
Journal: Cancer Research (2022)

Abstract KRAS is mutated in 35%-45% of colorectal cancers (CRC), and KRAS mutational status determines the prognosis and therapeutic options available to patients with advanced CRC. Direct KRASG12C inhibitors have proven to be highly effective for patients with non-small cell lung cancers, but unfortunately are relatively ineffective in the treatment of CRC. Thus, we have investigated tissue-specific mechanisms of resistance to direct KRAS inhibition. We used multiplex inhibitor bead kinome profiling (MIBs) and global phosphoproteomic analysis to determine the signaling response to the KRASG12C inhibitor ARS-1620 in four human colon cancer cell lines. Analyzing the kinome revealed a profound reprogramming beyond the Ras/MAPK pathway. We used network propagation to integrate analysis across these lines and define essential signaling nodes modified by direct KRAS inhibition, including two distinct signaling nodes containing RAS/MAPK and WNT-regulating kinases. Two additional smaller nodes contained WNK kinases and their effectors, followed by Hippo and a number of cell cycle-related kinases. The WNK kinases have been identified to modulate beta-catenin, a major driver of CRC biology, via the GID E3 ubiquitin ligase complex. Thus, to understand the signaling that links KRAS and beta-catenin, we used small molecule inhibitors of these kinases along with ARS-1620, we tested how they affected the transcription of beta-catenin targets. Additionally, we assessed the correlation between WNK/GID complex, and beta-catenin transcriptional output using western blot and quantitative real time PCR and observe that inhibition of KRASG12C also modulates beta-catenin transcriptional output. Our results identify new families of possible kinase targets in CRCs expressing KRAS mutations and shed light on the relationship of KRAS, beta-catenin, and WNK/GID in CRC maintenance. By dissecting these signaling relationships, we hope to identify potential drug combinations to overcome primary resistance KRASG12C inhibition in CRC. Citation Format: Kasturi Nayak, Yeonjoo Hwang, LeeAnn Wang, Danielle L. Swaney, Nevan J. Krogan, John D. Gordan. Inhibition of KRASG12C in colon cancer illustrates a link between beta-catenin, WNK, and the GID complex [abstract]. In: Proceedings of the AACR Special Conference on Colorectal Cancer; 2022 Oct 1-4; Portland, OR. Philadelphia (PA): AACR; Cancer Res 2022;82(23 Suppl_1):Abstract nr B016.
Abstract PR010: Inhibition of HGF maturation overcomes cetuximab resistance in colorectal cancer
Authors: Ramona Graves-Deal, Vivian T. Jones, Galina T. Bogatcheva, Zheng Cao, Sarah J. Harmych, Vishnu Damalanka, Lidija Klampfer, Robert J. Coffey, James W. Janetka, Bhuminder Singh
Journal: Cancer Research (2022)

Abstract We have previously identified that activation of receptor tyrosine kinases (RTKs), MET and RON contributed to resistance to the EGF receptor (EGFR)-directed therapeutic antibody, cetuximab. These findings originated from our in vitro 3D type I collagen cultures of human colorectal cancer (CRC) cell line HCA-7 derivatives CC, SC, and CC-CR. CC are sensitive to cetuximab, while SC and CC-CR are resistant. Both de novo and acquired modes of cetuximab resistance in SC and CC-CR, respectively, could be overcome by crizotinib, a multi-RTK inhibitor that also targets MET and RON. Conversely, exogenous administration of MET ligand, HGF could transiently induce cetuximab resistance which could be further overcome by crizotinib addition. HGF/HGFL are synthesized as inactive precursors and require cleavage by proteases (HGFA, Matriptase, and Hepsin) to be biologically active. To inhibit HGF/HGFL cleavage in cetuximab-resistant cells, we employed inhibitors of HGF/HGFL proteases (ZFH7116 and VD2173) and were able to overcome both de novo and acquired cetuximab resistance. A survey of TCGA datasets indicated that HGF/HGFL were overexpressed in several CRC CMS subtypes. We next expressed human HGF in cetuximab-sensitive CC cells and observed that HGF overexpression imparts cetuximab resistance. Moreover, cetuximab resistance induced by HGF overexpression could be overcome by the downstream MET inhibition (with crizotinib), and we are now testing if the upstream inhibition of HGF proteases (with ZFH7116/VD2173) also overcomes cetuximab resistance. Combined these results indicate that inhibition of HGF cleavage and maturation may be a novel way to overcome resistance to EGFR-targeted therapies in CRC. Citation Format: Ramona Graves-Deal, Vivian T. Jones, Galina T. Bogatcheva, Zheng Cao, Sarah J. Harmych, Vishnu Damalanka, Lidija Klampfer, Robert J. Coffey, James W. Janetka, Bhuminder Singh. Inhibition of HGF maturation overcomes cetuximab resistance in colorectal cancer [abstract]. In: Proceedings of the AACR Special Conference on Colorectal Cancer; 2022 Oct 1-4; Portland, OR. Philadelphia (PA): AACR; Cancer Res 2022;82(23 Suppl_1):Abstract nr PR010.
Abstract IA014: Synthetic essentiality identifies TDO2 as a key target in APC-deficient CRC
Authors: Rumi Lee, Jiexi Li, Jun Li, Chang-Jiun Wu, Shan Jiang, Wen-Hao Hsu, Deepavali Chakravarti, Peiwen Chen, Kyle A. LaBella, Jing Li, Denise J. Spring, Di Zhao, Y. Alan Wang, Ronald A. DePinho
Journal: Cancer Research (2022)

Abstract Loss of adenomatous polyposis coli (APC) is considered a critical initiating event in colorectal cancer (CRC), where it occurs in 90% of sporadic CRCs. APC deficiency results in activation of WNT; however, major hurdles persist to therapeutic intervention of this pathway. Here, the synthetic essentiality framework was used to discover other potential druggable vulnerabilities for APC-deficient cancers. Through this approach, tryptophan 2,3-dioxygenase 2 (TDO2) was identified as a synthetic essential effector of APC-deficient CRC. Upregulation of TDO2 activates the Kyn-AhR pathway, increasing glycolysis. Subsequent cancer cell growth and CXCL5 secretion leads to macrophage recruitment into the tumor microenvironment. APC-deficient CRC models were found to be susceptible to both TDO2 depletion and pharmacologic inhibition. Overall, this study identifies the TCF4-TDO2-AhR-CXCL5 axis as a critical pathway in the maintenance of APC-deficient CRC, informing potential genotype-specific therapeutic targets and the use of TDO2 inhibitors to combat this disease. Citation Format: Rumi Lee, Jiexi Li, Jun Li, Chang-Jiun Wu, Shan Jiang, Wen-Hao Hsu, Deepavali Chakravarti, Peiwen Chen, Kyle A. LaBella, Jing Li, Denise J. Spring, Di Zhao, Y. Alan Wang, Ronald A. DePinho. Synthetic essentiality identifies TDO2 as a key target in APC-deficient CRC [abstract]. In: Proceedings of the AACR Special Conference on Colorectal Cancer; 2022 Oct 1-4; Portland, OR. Philadelphia (PA): AACR; Cancer Res 2022;82(23 Suppl_1):Abstract nr IA014.
Abstract IA027: Recent advances in the study of extracellular vesicles and nanoparticles in colorectal cancer
Authors: Robert J. Coffey
Journal: Cancer Research (2022)

Abstract Extracellular vesicles (EVs) and nanoparticles (NPs) are increasingly recognized as important mediators of intercellular communication with implications for the diagnosis, monitoring and possibly treatment of colorectal cancer. We recently reviewed this topic in Gastroenterology. EVs are lipid bilayer-enclosed vesicles that can be classified as small (s) some of which are tetraspanin-containing, endosomally-derived exosomes (5-120 nm) and large that include plasma membrane-budding microvescles (150-800 nm). Nanoparticles are more recently discovered smaller amembranous nanoparticles that include exomeres (30-50 nm) and supermeres (25-35 nm). We have performed a comprehensive proteomic and RNA analysis of sEVs, exomeres and supermeres. Highlights from this analysis will be presented with a focus on their clinical relevance and the merits of parsing versus pooling biofluid fractions. Citation Format: Robert J. Coffey. Recent advances in the study of extracellular vesicles and nanoparticles in colorectal cancer [abstract]. In: Proceedings of the AACR Special Conference on Colorectal Cancer; 2022 Oct 1-4; Portland, OR. Philadelphia (PA): AACR; Cancer Res 2022;82(23 Suppl_1):Abstract nr IA027.
Abstract IA003: ctDNA Guiding adjuvant treatment in early stage colon cancer: Are we moving the needle?
Authors: Jeanne Tie
Journal: Cancer Research (2022)

Abstract My presentation will summarize the accumulating evidence on the ability of circulating tumor DNA to detect minimal residual disease and track adjuvant treatment efficacy in colorectal cancer and the potential for ctDNA to reshape the adjuvant treatment paradigm. I will also discuss the rationale and results of the DYNAMIC trial (ctDNA-guiding adjuvant therapy study in stage II colon cancer) and other ongoing ctDNA-based trials. Citation Format: Jeanne Tie. ctDNA Guiding adjuvant treatment in early stage colon cancer: Are we moving the needle? [abstract]. In: Proceedings of the AACR Special Conference on Colorectal Cancer; 2022 Oct 1-4; Portland, OR. Philadelphia (PA): AACR; Cancer Res 2022;82(23 Suppl_1):Abstract nr IA003.
Abstract A015: Targeting necroptosis and RIP3 in colorectal cancer to overcome chemotherapeutic resistance
Authors: Kaylee A. Ermine, Dongshi Chen, Peng Wang, Jian Yu, Lin Zhang
Journal: Cancer Research (2022)

Abstract Colorectal cancer (CRC) is the third most commonly diagnosed cancer in the United States. When metastatic, chemotherapeutic drug 5-fluorouracil (5-FU) is typically used for treatment, but resistance often occurs. Many studies have shown that 5-FU induces apoptosis in cancer cells, but when apoptosis is inhibited, cell death can still occur, suggesting that other forms of cell death are occurring. Necroptosis, or regulated necrosis, is an alternative form of cell death, controlled by RIP1, RIP3, and MLKL, and its role in anticancer therapy remains unclear. TCGA RNAseq data show that RIP3 is significantly downregulated in primary CRC tumors, with RIP3 downregulation correlating with worse clinical outcomes. Analysis of numerous established CRC cell lines revealed that RIP3 expression was downregulated in ~50% of the cell lines, with low RIP3 expression being associated with decreased 5-FU sensitivity. These data led us to hypothesize that RIP3 expression and necroptosis may play a critical role in response to anticancer therapies, such as 5-FU, and that restoring defective necroptosis may enhance therapeutic sensitivity. Our preliminary studies have shown that RIP3-expressing (RIP3+) CRC cell lines are able to undergo both apoptosis and necroptosis in response to 5-FU, which could explain the enhanced sensitivity. As expected, knock-out of RIP3 in RIP3+ cells resulted in decreased 5-FU sensitivity, as well as abrogated necroptosis induction. Additionally, transient restoration of RIP3 in RIP3-silenced (RIP3-) CRC cells appeared to enhance 5-FU sensitivity, and so, we generated a stable RIP3-expressing cell line through retroviral infection. Although the stable RIP3-expressing cell line did not appear to be more sensitive to 5-FU alone, it did show enhanced sensitivity under conditions where apoptosis is inhibited. Together, our results suggest that RIP3 plays an important role in 5-FU-induced cell death in CRC, and that restoring RIP3 when the apoptosis pathway is implicated could provide a way to enhance 5-FU sensitivity and overcome resistance. The results from this project provide novel insight into the role of RIP3 in mediating response to anticancer therapy in CRC, which could be used for development of improved therapies and personalized medicine based on RIP3 status in the clinic. Citation Format: Kaylee A. Ermine, Dongshi Chen, Peng Wang, Jian Yu, Lin Zhang. Targeting necroptosis and RIP3 in colorectal cancer to overcome chemotherapeutic resistance [abstract]. In: Proceedings of the AACR Special Conference on Colorectal Cancer; 2022 Oct 1-4; Portland, OR. Philadelphia (PA): AACR; Cancer Res 2022;82(23 Suppl_1):Abstract nr A015.
Abstract B031: The effects of tissue processing and microfluidic factors on single-cell RNA-sequencing data quality in colorectal tissues
Authors: Deronisha L. Arceneaux, Zhengyi Chen, Joey Simmons, Bob Chen, Cody Heiser, Yanwen Xu
Journal: Cancer Research (2022)

Abstract Our HTAN (Human Tumor Atlas Network) study presented in Chen et al. documented single-cell RNA-sequencing (scRNA-seq) data on 128 human colonic specimens for mapping out distinct paths for polyp to cancer transformations. What we have not detailed is our optimizations on the droplet-based scRNA-seq approach that generate high quality data from challenging tissues such as the colonic epithelium. In this work, we provide a systematic dissection of tissue processing and microfluidic encapsulation factors that affect data quality generated on colonic epithelial cells using an open droplet-based scRNA-seq platform (inDrops). We optimized our process based on these factors to significantly decrease dying cell bodies and ambient RNA from being co-encapsulated with true cells, which led to the development of the current scRNA-seq protocol used for human specimens. We have also developed pre-filtering data metrics to score data quality stemming from degree of ambient contamination. We envision that these experimental optimizations reduce the amount of introduced artifacts, leading to more rigorous biological interpretations. Citation Format: Deronisha L. Arceneaux, Zhengyi Chen, Joey Simmons, Bob Chen, Cody Heiser, Yanwen Xu. The effects of tissue processing and microfluidic factors on single-cell RNA-sequencing data quality in colorectal tissues [abstract]. In: Proceedings of the AACR Special Conference on Colorectal Cancer; 2022 Oct 1-4; Portland, OR. Philadelphia (PA): AACR; Cancer Res 2022;82(23 Suppl_1):Abstract nr B031.
Abstract IA005: Risk prediction in colorectal cancer screening: Reflections on the current status
Authors: Robert E. Schoen
Journal: Cancer Research (2022)

Abstract Colorectal cancer screening is an effective means of reducing colorectal cancer incidence and mortality. However, the testing we have, though effective, is costly and inefficient, with the majority of people undergoing an expensive, negative screening examination such as colonoscopy. Risk prediction is a potential means to tailor screening and personalize care to risk. Individuals could be directed to a less invasive test (FIT or blood testing) as opposed to a more invasive test (colonoscopy), or to other adjustments such as modifying the starting age for screening. The polygenic risk score is an objective, reproducible risk assessment tool, that has promise, but its utility and possible application in clinical practice will require considerably more investigation. Other challenges include determining the “threshold“ for assignment to a low risk as opposed to a high risk screening strategy, and ensuring that risk assessment does not deter subsequent screening behavior. Citation Format: Robert E. Schoen. Risk prediction in colorectal cancer screening: Reflections on the current status [abstract]. In: Proceedings of the AACR Special Conference on Colorectal Cancer; 2022 Oct 1-4; Portland, OR. Philadelphia (PA): AACR; Cancer Res 2022;82(23 Suppl_1):Abstract nr IA005.
Abstract B032: Native sgRNA capture and sequencing (NSC-seq) reveals tumor formation in ApcMin/+ mice and in human colorectal cancer is an oligoclonal process
Authors: Mirazul Islam, Yilin Yang, Vishal M. Shah, Alan J. Simmons, Yanwen Xu, Robert J. Coffey, Ken S. Lau
Journal: Cancer Research (2022)

Abstract CRISPR-Cas9-based technologies have been developed to address a wide range of biological questions, including molecular recording of embryonic development, genetic screening, and tracking tumor evolution at the single-cell resolution. We developed a single-cell lineage tracking platform called native sgRNA Capture and sequencing (NSC-seq) to leverage CRISPR technology for clonal analysis of intestinal tumors in the ApcMin/+ mouse model. We combined CRISPR-induced mutations with spontaneously accumulating mitochondrial variants to enable highly efficient lineage-tracking of single cells. We generated lineage-tracked ApcMin/+ tumors and found that there are more than two independently arising clones within a tumor. We also found oligoclonal tumors within human colorectal specimens using this technology, supporting the oligoclonality of intestinal tumor development across species. Finally, we demonstrated the application of this technology in understanding the rate of loss-of-heterozygosity events in Apc as related to the cellular turnover rates of different intestinal regions. Overall, NSC-seq enables in vivo molecular recording of spontaneous intestinal tumor development at single-cell resolution. Citation Format: Mirazul Islam, Yilin Yang, Vishal M. Shah, Alan J. Simmons, Yanwen Xu, Robert J. Coffey, Ken S. Lau. Native sgRNA capture and sequencing (NSC-seq) reveals tumor formation in ApcMin/+ mice and in human colorectal cancer is an oligoclonal process [abstract]. In: Proceedings of the AACR Special Conference on Colorectal Cancer; 2022 Oct 1-4; Portland, OR. Philadelphia (PA): AACR; Cancer Res 2022;82(23 Suppl_1):Abstract nr B032.
Abstract B022: The NEDD8 pathway as a therapeutic target in HER2-amplified colorectal cancer
Authors: Federica Invrea, Alessandro Carugo, Consalvo Petti, Giulio Draetta, Enzo Medico
Journal: Cancer Research (2022)

Abstract Colorectal cancer (CRC) is a heterogeneous disease with a wide spectrum of clinical outcomes, from indolent resectable disease to aggressive-metastatic cases. Primary and acquired resistance limits the efficacy of available treatments, and the identification of effective drug combinations is needed to further improve patients' outcomes. We previously found that the NEDD8-activating enzyme inhibitor pevonedistat induces tumor stabilization in preclinical models of poorly differentiated, clinically aggressive CRC resistant to available therapies. To identify drugs that can be effectively combined with pevonedistat, we performed a drop-out loss-of-function synthetic lethality screening with a shRNA library covering 200 drug-target genes in four different CRC cell lines. Multiple screening hits were found to be involved in the EGFR signaling pathway, suggesting that, rather than inhibition of a specific gene, interference with the EGFR pathway at various levels could be effectively leveraged for combination therapies based on pevonedistat. Exploiting both BRAF-mutant and RAS/RAF wild-type CRC models, we validated the therapeutic relevance of our findings by showing that combined blockade of NEDD8 and EGFR pathways led to increased growth arrest and apoptosis both in vitro and in vivo. Pathway modulation analysis showed that compensatory feedback loops induced by single treatments were blunted by the combinations. Our results suggested possible therapeutic opportunities in specific CRC clinical settings. We further focused on HER2-amplified CRC and found marked sensitivity to pevonedistat in a CRC cell line carrying HER2 amplification. In these cells, long-term in vitro treatment with a combination of lapatinib and trastuzumab induces the emergence of colonies of long-term persisters (i.e., cells surviving to several weeks of HER2/EGFR blockade). These persisters display extremely slow growth and senescence features, however they fully recover upon removal of the blockade, mimicking disease relapse in patients after treatment suspension. Interestingly, persister colonies maintained sensitivity to pevonedistat, displaying a marked decrease when pevonedistat was added after six weeks of HER2/EGFR blockade, independently of the continuation of the blockade. These results unveil the possibility of employing pevonedistat in HER2-amplified CRC patients subsequently to tumor stabilization or regression by HER-2/EGFR blockade. Citation Format: Federica Invrea, Alessandro Carugo, Consalvo Petti, Giulio Draetta, Enzo Medico. The NEDD8 pathway as a therapeutic target in HER2-amplified colorectal cancer [abstract]. In: Proceedings of the AACR Special Conference on Colorectal Cancer; 2022 Oct 1-4; Portland, OR. Philadelphia (PA): AACR; Cancer Res 2022;82(23 Suppl_1):Abstract nr B022.
Abstract IA010: Patient derived organoids in precision oncology
Authors: Nicola Valeri
Journal: Cancer Research (2022)

Abstract Limits in the predictive power of molecular profiling and shortcomings of some pre-clinical models used in drug development represent important obstacles hampering the success of personalized medicine and drug discovery. LGR5+ stem cells can be isolated from a number of organs and propagated as epithelial organoids in vitro. Mouse and human organoids have been used to study the physiology and neoplastic transformation of the liver, pancreas, bowel and prostate among other organs. During my talk, I will highlight opportunities, limitations and potential clinical applications of patient-derived organoids in personalized oncology, emphasizing strengths and hurdles in the use of the organoid technology in forward and reverse translational cancer research. In particular, I will stress the importance of patient-derived organoids as pre-clinical tools to define mechanisms of drug resistance and to design novel drug combinations. Citation Format: Nicola Valeri. Patient derived organoids in precision oncology [abstract]. In: Proceedings of the AACR Special Conference on Colorectal Cancer; 2022 Oct 1-4; Portland, OR. Philadelphia (PA): AACR; Cancer Res 2022;82(23 Suppl_1):Abstract nr IA010.